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Convert to PEtab v2 #270

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7259a65
Convert to PEtab v2
dweindl Jul 14, 2025
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dweindl Jul 22, 2025
24ebe2a
convert
dweindl Jul 22, 2025
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dweindl Oct 16, 2025
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dweindl Jul 10, 2026
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35 changes: 35 additions & 0 deletions v1_v2.py
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#!/usr/bin/env python3
"""Convert benchmark problems from PEtab v1 to v2 format."""

import logging
import benchmark_models_petab
from petab.v2.petab1to2 import petab1to2
from pathlib import Path

def main():
logging.basicConfig(level=logging.INFO)
v2_root = Path(__file__).resolve().parent / "v2"

for problem_id in benchmark_models_petab.MODELS:
if problem_id == "Froehlich_CellSystems2018":
# naive conversion generates huge condition table
logging.warning("Skipping Froehlich_CellSystems2018 due to performance issues.")
continue

convert(problem_id, output_dir=v2_root / problem_id)

def convert(problem_id: str, output_dir: Path):
"""Convert a PEtab v1 problem to v2 format."""
logging.info(f"Converting {problem_id}...")
yaml_path = benchmark_models_petab.get_problem_yaml_path(problem_id)
try:
petab1to2(yaml_path, output_dir)
except NotImplementedError as e:
logging.warning(f"Skipping {problem_id}: {e}")
return

logging.info(f"Converted {problem_id}.")


if __name__ == "__main__":
main()
17 changes: 17 additions & 0 deletions v2/Alkan_SciSignal2018/Alkan_SciSignal2018.yaml
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format_version: 2.0.0
parameter_files:
- parameters_Alkan_SciSignal2018.tsv
model_files:
model_Alkan_SciSignal2018:
location: model_Alkan_SciSignal2018.xml
language: sbml
measurement_files:
- measurementData_Alkan_SciSignal2018.tsv
condition_files:
- experimentalCondition_Alkan_SciSignal2018.tsv
experiment_files:
- experiments.tsv
observable_files:
- observables_Alkan_SciSignal2018.tsv
mapping_files: []
extensions: {}
220 changes: 220 additions & 0 deletions v2/Alkan_SciSignal2018/experimentalCondition_Alkan_SciSignal2018.tsv
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conditionId targetId targetValue
model1_data1 Dox_level 0.0
model1_data2 Dox_level 0.0
model1_data3 Dox_level 0.0
model1_data4 Dox_level 0.0
model1_data5 Dox_level 0.0
model1_data6 Dox_level 0.0
model1_data8 Dox_level 0.0016
model1_data9 Dox_level 0.008
model1_data10 Dox_level 0.04
model1_data11 Dox_level 0.2
model1_data12 Dox_level 1.0
model1_data14 Dox_level 0.0
model1_data15 Dox_level 0.0
model1_data16 Dox_level 0.0
model1_data17 Dox_level 0.0
model1_data18 Dox_level 0.0
model1_data20 Dox_level 0.01
model1_data21 Dox_level 0.05
model1_data22 Dox_level 0.1
model1_data25 Dox_level 0.0
model1_data26 Dox_level 0.0
model1_data29 Dox_level 0.0
model1_data30 Dox_level 0.0
model1_data32 Dox_level 0.00078125
model1_data33 Dox_level 0.0012346
model1_data34 Dox_level 0.0015625
model1_data35 Dox_level 0.003125
model1_data36 Dox_level 0.0037037
model1_data37 Dox_level 0.00625
model1_data38 Dox_level 0.011111
model1_data39 Dox_level 0.0125
model1_data40 Dox_level 0.025
model1_data41 Dox_level 0.033333
model1_data44 Dox_level 0.3
model1_data46 Dox_level 0.0
model1_data47 Dox_level 0.0
model1_data48 Dox_level 0.0
model1_data49 Dox_level 0.0
model1_data50 Dox_level 0.0
model1_data51 Dox_level 0.0
model1_data52 Dox_level 0.0
model1_data53 Dox_level 0.0
model1_data54 Dox_level 0.0
model1_data55 Dox_level 0.0
model1_data58 Dox_level 0.0
model1_data60 Dox_level 0.0
model1_data61 Dox_level 0.0
model1_data62 Dox_level 0.0
model1_data63 Dox_level 0.0
model1_data64 Dox_level 0.0
model1_data65 Dox_level 0.0
model1_data66 Dox_level 0.0
model1_data67 Dox_level 0.0
model1_data68 Dox_level 0.0
model1_data69 Dox_level 0.0
model1_data72 Dox_level 0.0
model1_data73 Dox_level 0.0
model1_data74 Dox_level 0.0
model1_data75 Dox_level 0.0
model1_data76 Dox_level 0.0
model1_data77 Dox_level 0.0
model1_data78 Dox_level 0.0
model1_data79 Dox_level 0.004
model1_data80 Dox_level 0.012
model1_data81 Dox_level 0.037
model1_data82 Dox_level 0.111
model1_data83 Dox_level 0.333
model1_data85 Dox_level 0.0
model1_data86 Dox_level 0.0
model1_data87 Dox_level 0.0
model1_data88 Dox_level 0.0
model1_data89 Dox_level 0.0
model1_data90 Dox_level 0.0
model1_data1 Gem_level 0.0
model1_data2 Gem_level 0.0003
model1_data3 Gem_level 0.002
model1_data4 Gem_level 0.01
model1_data5 Gem_level 0.04
model1_data6 Gem_level 6e-05
model1_data8 Gem_level 0.0
model1_data9 Gem_level 0.0
model1_data10 Gem_level 0.0
model1_data11 Gem_level 0.0
model1_data12 Gem_level 0.0
model1_data14 Gem_level 0.0
model1_data15 Gem_level 0.0
model1_data16 Gem_level 0.0
model1_data17 Gem_level 0.0
model1_data18 Gem_level 0.0
model1_data20 Gem_level 0.0
model1_data21 Gem_level 0.0
model1_data22 Gem_level 0.0
model1_data25 Gem_level 0.0
model1_data26 Gem_level 0.0
model1_data29 Gem_level 0.05
model1_data30 Gem_level 0.1
model1_data32 Gem_level 0.0
model1_data33 Gem_level 0.0
model1_data34 Gem_level 0.0
model1_data35 Gem_level 0.0
model1_data36 Gem_level 0.0
model1_data37 Gem_level 0.0
model1_data38 Gem_level 0.0
model1_data39 Gem_level 0.0
model1_data40 Gem_level 0.0
model1_data41 Gem_level 0.0
model1_data44 Gem_level 0.0
model1_data46 Gem_level 0.0
model1_data47 Gem_level 0.0
model1_data48 Gem_level 0.0
model1_data49 Gem_level 0.0
model1_data50 Gem_level 0.0
model1_data51 Gem_level 0.0
model1_data52 Gem_level 0.0
model1_data53 Gem_level 0.0
model1_data54 Gem_level 0.0
model1_data55 Gem_level 0.0
model1_data58 Gem_level 0.0
model1_data60 Gem_level 0.00078125
model1_data61 Gem_level 0.0012346
model1_data62 Gem_level 0.0015625
model1_data63 Gem_level 0.003125
model1_data64 Gem_level 0.0037037
model1_data65 Gem_level 0.00625
model1_data66 Gem_level 0.011111
model1_data67 Gem_level 0.0125
model1_data68 Gem_level 0.025
model1_data69 Gem_level 0.033333
model1_data72 Gem_level 0.3
model1_data73 Gem_level 0.001
model1_data74 Gem_level 0.004
model1_data75 Gem_level 0.012
model1_data76 Gem_level 0.037
model1_data77 Gem_level 0.111
model1_data78 Gem_level 0.333
model1_data79 Gem_level 0.0
model1_data80 Gem_level 0.0
model1_data81 Gem_level 0.0
model1_data82 Gem_level 0.0
model1_data83 Gem_level 0.0
model1_data85 Gem_level 0.0
model1_data86 Gem_level 0.0
model1_data87 Gem_level 0.0
model1_data88 Gem_level 0.0
model1_data89 Gem_level 0.0
model1_data90 Gem_level 0.0
model1_data1 SN38_level 0.0
model1_data2 SN38_level 0.0
model1_data3 SN38_level 0.0
model1_data4 SN38_level 0.0
model1_data5 SN38_level 0.0
model1_data6 SN38_level 0.0
model1_data8 SN38_level 0.0
model1_data9 SN38_level 0.0
model1_data10 SN38_level 0.0
model1_data11 SN38_level 0.0
model1_data12 SN38_level 0.0
model1_data14 SN38_level 0.0003
model1_data15 SN38_level 0.002
model1_data16 SN38_level 0.01
model1_data17 SN38_level 0.04
model1_data18 SN38_level 6e-05
model1_data20 SN38_level 0.0
model1_data21 SN38_level 0.0
model1_data22 SN38_level 0.0
model1_data25 SN38_level 0.05
model1_data26 SN38_level 0.1
model1_data29 SN38_level 0.0
model1_data30 SN38_level 0.0
model1_data32 SN38_level 0.0
model1_data33 SN38_level 0.0
model1_data34 SN38_level 0.0
model1_data35 SN38_level 0.0
model1_data36 SN38_level 0.0
model1_data37 SN38_level 0.0
model1_data38 SN38_level 0.0
model1_data39 SN38_level 0.0
model1_data40 SN38_level 0.0
model1_data41 SN38_level 0.0
model1_data44 SN38_level 0.0
model1_data46 SN38_level 0.00078125
model1_data47 SN38_level 0.0012346
model1_data48 SN38_level 0.0015625
model1_data49 SN38_level 0.003125
model1_data50 SN38_level 0.0037037
model1_data51 SN38_level 0.00625
model1_data52 SN38_level 0.011111
model1_data53 SN38_level 0.0125
model1_data54 SN38_level 0.025
model1_data55 SN38_level 0.033333
model1_data58 SN38_level 0.3
model1_data60 SN38_level 0.0
model1_data61 SN38_level 0.0
model1_data62 SN38_level 0.0
model1_data63 SN38_level 0.0
model1_data64 SN38_level 0.0
model1_data65 SN38_level 0.0
model1_data66 SN38_level 0.0
model1_data67 SN38_level 0.0
model1_data68 SN38_level 0.0
model1_data69 SN38_level 0.0
model1_data72 SN38_level 0.0
model1_data73 SN38_level 0.0
model1_data74 SN38_level 0.0
model1_data75 SN38_level 0.0
model1_data76 SN38_level 0.0
model1_data77 SN38_level 0.0
model1_data78 SN38_level 0.0
model1_data79 SN38_level 0.0
model1_data80 SN38_level 0.0
model1_data81 SN38_level 0.0
model1_data82 SN38_level 0.0
model1_data83 SN38_level 0.0
model1_data85 SN38_level 0.004
model1_data86 SN38_level 0.012
model1_data87 SN38_level 0.037
model1_data88 SN38_level 0.111
model1_data89 SN38_level 0.333
model1_data90 SN38_level 1.0
74 changes: 74 additions & 0 deletions v2/Alkan_SciSignal2018/experiments.tsv
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experimentId time conditionId
experiment____model1_data1 0 model1_data1
experiment____model1_data10 0 model1_data10
experiment____model1_data11 0 model1_data11
experiment____model1_data12 0 model1_data12
experiment____model1_data14 0 model1_data14
experiment____model1_data15 0 model1_data15
experiment____model1_data16 0 model1_data16
experiment____model1_data17 0 model1_data17
experiment____model1_data18 0 model1_data18
experiment____model1_data2 0 model1_data2
experiment____model1_data20 0 model1_data20
experiment____model1_data21 0 model1_data21
experiment____model1_data22 0 model1_data22
experiment____model1_data25 0 model1_data25
experiment____model1_data26 0 model1_data26
experiment____model1_data29 0 model1_data29
experiment____model1_data3 0 model1_data3
experiment____model1_data30 0 model1_data30
experiment____model1_data32 0 model1_data32
experiment____model1_data33 0 model1_data33
experiment____model1_data34 0 model1_data34
experiment____model1_data35 0 model1_data35
experiment____model1_data36 0 model1_data36
experiment____model1_data37 0 model1_data37
experiment____model1_data38 0 model1_data38
experiment____model1_data39 0 model1_data39
experiment____model1_data4 0 model1_data4
experiment____model1_data40 0 model1_data40
experiment____model1_data41 0 model1_data41
experiment____model1_data44 0 model1_data44
experiment____model1_data46 0 model1_data46
experiment____model1_data47 0 model1_data47
experiment____model1_data48 0 model1_data48
experiment____model1_data49 0 model1_data49
experiment____model1_data5 0 model1_data5
experiment____model1_data50 0 model1_data50
experiment____model1_data51 0 model1_data51
experiment____model1_data52 0 model1_data52
experiment____model1_data53 0 model1_data53
experiment____model1_data54 0 model1_data54
experiment____model1_data55 0 model1_data55
experiment____model1_data58 0 model1_data58
experiment____model1_data6 0 model1_data6
experiment____model1_data60 0 model1_data60
experiment____model1_data61 0 model1_data61
experiment____model1_data62 0 model1_data62
experiment____model1_data63 0 model1_data63
experiment____model1_data64 0 model1_data64
experiment____model1_data65 0 model1_data65
experiment____model1_data66 0 model1_data66
experiment____model1_data67 0 model1_data67
experiment____model1_data68 0 model1_data68
experiment____model1_data69 0 model1_data69
experiment____model1_data72 0 model1_data72
experiment____model1_data73 0 model1_data73
experiment____model1_data74 0 model1_data74
experiment____model1_data75 0 model1_data75
experiment____model1_data76 0 model1_data76
experiment____model1_data77 0 model1_data77
experiment____model1_data78 0 model1_data78
experiment____model1_data79 0 model1_data79
experiment____model1_data8 0 model1_data8
experiment____model1_data80 0 model1_data80
experiment____model1_data81 0 model1_data81
experiment____model1_data82 0 model1_data82
experiment____model1_data83 0 model1_data83
experiment____model1_data85 0 model1_data85
experiment____model1_data86 0 model1_data86
experiment____model1_data87 0 model1_data87
experiment____model1_data88 0 model1_data88
experiment____model1_data89 0 model1_data89
experiment____model1_data9 0 model1_data9
experiment____model1_data90 0 model1_data90
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